This is a major development. Holy crap.
To the developers: you've got a lot of power. You're going to shape the future of Wii homebrew. So, I have a request: do it elegantly. What do I mean, elegantly?
1) For the three files - the icon, the metadata and the ELF - put them into App bundles / App directories a la ROX Desktop and Mac OS X. Basically, what you do is you treat directories that end with ".app" (or maybe ".wiiapp") differently from a normal directory. Take a look here:
http://en.wikipedia.org/wiki/Bundle_(NEXTSTEP)
2) Wii homebrew developers should standardize the location of things in the filesystem. One of my major pet peeves about DS homebrew is that programs with config files just save the config files to wherever they damn well want. We should push developers to save their configs and such to, let's say, /Config/Appname/. Think /etc/ in Unix.
Godspeed, homebrew channel team. Godspeed.